July 22, 2012

Computer Model Maps Organism’s Entire Lifespan Completed

In what is being called "a breakthrough effort for computational biology," researchers from a pair of US universities have successfully completed a software model of an organism's entire lifespan.

The research, which was led by Stanford University Assistant Professor of Bioengineering Markus Covert, used data obtained from over 900 previous scientific papers in order to account for every molecular interaction that occurs during the life cycle of the single-celled Mycoplasma genitalium, Max McClure of the California institution said in a July 19 report.

Covert's team, which also included scientists from the J. Craig Venter Institute (JCVI), then completed a computerized model of the world's smallest free-living bacterium, which typically lives in the human genital and respiratory tracts, John Markoff of the New York Times wrote on Friday.

According to Stanford, their work, which is detailed in the journal Cell, "fulfills a longstanding goal for the field. Not only does the model allow researchers to address questions that aren't practical to examine otherwise, it represents a stepping-stone toward the use of computer-aided design in bioengineering and medicine."

Likewise, Markoff reports that experts believe the research represents a tremendous advance in the development of computerized laboratories, which theoretically could conduct thousands of experiments much more quickly than currently possible. It could also help the medical field in their fight against cancer, neurodegenerative diseases, and other serious diseases, while speeding-up the early stages of screening for new compounds and aiding the research of molecular biologists in the process, the Times reporter added.

"This achievement demonstrates a transforming approach to answering questions about fundamental biological processes," James M. Anderson, director of the National Institutes of Health (NIH) Division of Program Coordination, Planning and Strategic Initiatives (DPCPSI), said in a statement. "Comprehensive computer models of entire cells have the potential to advance our understanding of cellular function and, ultimately, to inform new approaches for the diagnosis and treatment of disease."

"The model presented by the authors is the first truly integrated effort to simulate the workings of a free-living microbe, and it should be commended for its audacity alone," a pair of independent commentators, Peter L. Freddolino and Saeed Tavazoie, both of Columbia University, wrote in an editorial accompanying the article, according to Markoff. "This is a tremendous task, involving the interpretation and integration of a massive amount of data."

While Covert and his colleagues have called their work, which detailed all 525 genes of the Mycoplasma genitalium, a first draft, they told the Times that it was nonetheless the first time the entire life of a living organism had been so modeled using a computer simulation.

The program responsible for the model operated on a 128-computer cluster and charted the molecular interactions of the single-cellular bacterium in 28 different categories, including DNA, RNA, proteins, and metabolites, Markoff added, and while the genome of their current subject is the smallest in the world, Covert suggests that his team is planning bigger and better things.

“The real question on our minds is: what happens when we bring this to a bigger organism, like E. coli, yeast or even eventually a human cell?” he said, according to the Times. “I´ll have the answer in a couple of years."